Programme
Programme
The scientific program includes keynotes by leading researchers in the field (Dr Catherine Lozupone and Dr Andrey Rzhetsky).
Programme
Monday, 15 July 2024
10:40 | CAMDA Welcome & Overview | |
11:00 | CAMDA Keynote: Exploring drivers of gut microbiome compositional differences in disease and mechanistic pathways to recovery using big data | Catherine Lozupone, University of Colorado, U.S.A. |
12:20 | Lunch and Posters | |
14:20 | The Gut Microbiome based Health Index Challenge - Introduction | Kinga Zielińska, Małopolska Centre of Biotechnology, Jagiellonian University, Poland |
14:50 | Integrating Taxonomic and Functional Features for Gut Microbiome Health Indexing | Nelly Selem Mojica, Centro de Ciencias Matemáticas UNAM, Mexico |
15:20 | Using Gradient Boosting to Predict Health States from Composition and Function of the Gut Microbiome | Patrick Smyth, National Microbiology Laboratory, Canada |
15:40 | Microbiome time series data reveal predictable patterns of change | Zuzanna Karwowska, Małopolska Centre of Biotechnology, Jagiellonian University, Poland |
16:00 | Break, Open Networking Time | |
16:40 | CAMDA Invited: Prediction in microbiome science | Jesse Shapiro, McGill University, Montreal, Canada |
17:10 | The Elephant in the Room: Software and Hardware Security Vulnerabilities of Portable Sequencing Devices | Carson Stillman, University of Florida, U.S.A. |
17:20 | Improving genomic epidemiology of Giardia intestinalis with a core genome gene-by-gene subtyping schema | Miguel Prieto, Simon Fraser University, Canada |
17:30 | Analysis of Inverted Repeats in Viral Genomes at a Large Scale | Madhavi Ganapathiraju, Carnegie Mellon University, Qatar |
17:40 | Integration of Spatial Transcriptomics into Multimodal Imaging of Skin Aging | Christina Bauer, Medical University of Vienna & University of Applied Science, Krems, Austria |
17:50 | 1st day summary | |
18:15 | Leaving for CAMDA dinner | Marché des Éclusiers |
Tuesday, 16 July 2024
8:40 | CAMDA Keynote: Computational dissection of complex human disease | Andrey Rzhetsky, University of Chicago, U.S.A. |
10:00 | Coffee break | |
10:40 | The Synthetic Clinical Health Records Challenge - Introduction | Joaquin Dopazo, Andalusian Public Foundation Progress and Health-FPS, and University Hospital Virgen del Rocío/CSIC/University of Sevilla, Seville, Spain |
11:10 | Predicting Diabetes Complications from Electronic Health Record Visits Using Machine Learning Algorithms | Daniel Voskergian, Al-Quds University, Palestine |
11:30 | Cluster-based machine learning prediction of diabetes complications | Daniel Santana-Quinteros, Universidad Nacional Autónoma de México, Mexico |
11:50 | Measures for the Evaluation of Clustering Methods on Single Cell Data | Owen Visser, University of Florida, U.S.A. |
12:20 | Lunch and Posters | |
14:20 | The Anti-Microbial Resistance Prediction Challenge - Introduction | Paweł Łabaj, Małopolska Centre of Biotechnology, Jagiellonian University, Poland |
14:25 | The Antimicrobial Resistance Prediction Challenge | Alper Yurtseven, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbruecken, Germany |
14:55 | Machine learning models for AMR prediction | Jaime Salvador López Viveros, CCM UNAM, Mexico |
15:15 | ISMB Proceedings: Biomarker identification by interpretable Maximum Mean Discrepancy | Dexiong Chen, Max Planck Institue of Biochemistry, Germany |
15:35 | CAMDA Trophy ceremony | |
15:45 | CAMDA summary and closing remarks |
Keynotes
Dr Catherine Lozupone
Professor in the Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, U.S.A.
Title: Exploring drivers of gut microbiome compositional differences in disease and mechanistic pathways to recovery using big data
Abstract: The commensal gut microbiome plays an essential role in protecting against opportunistic pathogens and maintaining immune homeostasis. Dysbiosis, an imbalance in microbial communities, is linked with disease when this imbalance disturbs microbiota functions essential for maintaining health or introduces processes that promote disease. By performing meta-analyses of many studies that have sequenced the 16S ribosomal RNA gene to characterize gut microbial communities in different disease and health contexts, we have defined very young age and Western versus Developing world/Agrarian cultures to be two major axes of gut microbiome compositional variation that are important for explaining variability across healthy humans. Interestingly, among Western adults, individuals with different diseases or microbiome disturbances have migration along both of these major axes of health-associated gut microbiome variation. For instance, obese Western individuals sometimes have microbiomes that cluster closer to Prevotella-rich/Bacteroides-poor microbiome types in the developing world and this is more common in African versus European Americans. Related to age, gut microbiomes of adults with recurrent Clostridioides difficile infection, Inflammatory Bowel Disease, cancer, and intake of broad-spectrum antibiotics all tend to cluster closer to healthy infant gut microbiomes, characterized by low diversity with increased representation of facultative versus strict anaerobes. The relationship between highly disturbed and infant gut microbiome compositions is likely related to parallel processes that occur in primary versus secondary ecological succession, where absence of a complex community of healthy gut commensals allows for the colonization of opportunistic, early succession adapted organism that undergo an ordered turnover of membership. By coupling co-occurrence patterns and longitudinal analyses of dense time-series data with genomic and metabolic network interrogations to explore underlying drivers of microbial cooperation and competition, we have been generating hypotheses regarding important interactions that occur during succession and testing them in humanized mice.
About a speaker: Dr Lozupone is a Professor in the Department of Biomedical Informatics at the University of Colorado Anschutz Medical Campus. Her research focuses on the complex community of microorganisms that inhabit the gastrointestinal tract. She has been heavily involved in the development of popular computational tools for microbial community analysis, such as the UniFrac algorithm for comparing microbial diversity among many samples using phylogenetic information. Dr. Lozupone runs an NIH funded research group that integrates integrative bioinformatics analysis of multi-omic data with experimental confirmation. Her lab is currently working to understand microbiome composition and function in a variety of disease contexts, with an emphasis on the interaction between the gut microbiome, local and systemic immune phenotypes, and metabolic co-morbidity in HIV-infected individuals and on dietary strategies to prevent Clostridioides difficile infection.
Dr Andrey Rzhetsky
Edna K. Papazian Professor of Medicine and Human Genetics, University of Chicago, U.S.A.
Title: Computational dissection of complex human disease
About a speaker: Dr Andrey Rzhetsky is an Edna K. Papazian Professor of Medicine and Human Genetics at the University of Chicago. He is also a Pritzker Scholar, and a Senior Fellow at the Institute for Genomics and Systems Biology at the University of Chicago. His research is focused on computational dissection of etiology of complex human diseases.
I will cover a collection of interrelated topics in dissection of etiology of complex human diseases, as seen through lens of large-scale medical data analysis. Individual studies that I will cover focus on mosaic of genetic, environmental, and genetic—environmental interaction factors. The studies relied on massive medical records from US, Sweden, Denmark, and Japan, and a battery of modeling approaches